pval_qqplot: Quantile-quantile plot

In bryancquach/omixjutsu: Utilities for omics analysis tasks

Quantile-quantile plot

Description

Plots observed vs. expected p-values.

Usage

pval_qqplot(
  pvalues,
  outliers = NULL,
  sig_cutoff = 0.05,
  plot_lambda = T,
  df = 1
)

Arguments

pvalues	A vector of pvalues with associated feature IDs.
outliers	A vector of outlier IDs that correspond to the names in 'pvalues'.
sig_cutoff	Adjusted p-value significance threshold.
plot_lambda	If 'TRUE' calculate the genomic inflation factor and overlay it on the plot.
df	Degrees of freedom on the theoretical distribution. Used in calculating the genomic inflation factor. Only relevant when plot_lambda is 'TRUE'.

Details

Plot observed p-values vs. expected p-values. Expected p-values are assumed to follow a uniform distribution.

Value

A ggplot object.

bryancquach/omixjutsu documentation built on Jan. 29, 2023, 3:47 p.m.